[gmx-users] gromacs.org_gmx-users Digest, Vol 191, Issue 42
McDonnell, Thomas
thomas.mcdonnell.11 at ucl.ac.uk
Wed Mar 18 00:33:19 CET 2020
Re Gromacs NDG BGLC error.
Dear Justin
Apologies for not being clearer. NDG was from the crystal structure, CHARM GUI has replaced it with BGLC which is also not recognized. Could you advise me which forcefield would be best for this or how to modify my inputs?
Thanks
Thomas
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From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se>
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Subject: gromacs.org_gmx-users Digest, Vol 191, Issue 42
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Today's Topics:
1. Re: Gromax NDG/BGLC Force field Error (Justin Lemkul)
2. Fwd: Reproducibility of a PMF plot (Alex)
3. Extraction of frames at different interval (Farida Aziz)
4. Re: Fwd: Reproducibility of a PMF plot (Andr? Farias de Moura)
5. About membrane leaflets and msd (Poncho Arvayo Zatarain)
6. About gmx msd and membrane leaflets (Poncho Arvayo Zatarain)
----------------------------------------------------------------------
Message: 1
Date: Tue, 17 Mar 2020 13:04:08 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Gromax NDG/BGLC Force field Error
Message-ID: <f2370e1e-374a-aa6f-3d38-22267327476f at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 3/17/20 12:57 PM, McDonnell, Thomas wrote:
> Hey
>
> I am trying to do some MD of a glycoprotein, I've inputted the glycans through Charm-GUI online, but when I try to run simulations using any of the amber or charm forcefields, it throws up the error does not recognise NDG. My glycan pattern is:
>
> N-Acetylglucosamine, N-Acetylglucosamine, Mannose (branch) (Mannose, N Acetylglucosamine, Galactose ) x2
>
> How do I modify the input files to overcome this, or is there a different forcefield I should be using?
What is NDG? There is no such residue or patch in the CHARMM force field
so I don't know why CHARMM-GUI produced any file with such a residue name.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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------------------------------
Message: 2
Date: Tue, 17 Mar 2020 13:14:29 -0400
From: Alex <alexanderwien2k at gmail.com>
To: gmx-users at gromacs.org
Subject: [gmx-users] Fwd: Reproducibility of a PMF plot
Message-ID:
<CAEDv6u5tnNvtKRAG=f81pqYWxgC-4649qzwm6-OTyCJOhcaV4w at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Any comment, please?
Thank you,
Alex
---------- Forwarded message ---------
From: Alex <alexanderwien2k at gmail.com>
Date: Sun, Mar 15, 2020 at 8:16 PM
Subject: Reproducibility of a PMF plot
To: <gmx-users at gromacs.org>
Dear all,
Of course it is always good to prove that a MD simulation is reproducible
by repeating several replicas of a simulation and then average over the
quantity of interest, specially for a publishable result.
I wonder if that also is necessary for a potential of mean force (PMF)
calculation using umbrella sampling in which the bootstrap analysis is
performed to calculate the standard deviation?
Or for an alchemical free energy calculation where the e.g. the block
averaging is used?
Regards,
Alex
------------------------------
Message: 3
Date: Tue, 17 Mar 2020 18:39:11 +0000 (UTC)
From: Farida Aziz <faridaaziz90 at yahoo.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Extraction of frames at different interval
Message-ID: <106680237.4263419.1584470351171 at mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8
?Hey,?To extract the first frame (t = 0 ns) of the trajectory i have used the below command?
gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start.pdb -dump 0
?to extract the frames at 6000 ps, 8600 ps and 9500 ps the following command i adjust like below, are these ok?
gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start1.pdb -dump 6000
gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start.2pdb -dump 8600
gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start3.pdb -dump 9500
------------------------------
Message: 4
Date: Tue, 17 Mar 2020 15:10:38 -0300
From: Andr? Farias de Moura <moura at ufscar.br>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Fwd: Reproducibility of a PMF plot
Message-ID:
<CAKTwKgoP+BPEu1Df0GT_2rp15VySQYW5JdUkeFWVGFfL=Tt4-Q at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear Alex,
in a nutshell: yes, convergence might not have been achieved even if the
estimated error bars seem small.
maybe this reference might be helpful:
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1016%2Fj.bbamem.2016.03.006&data=02%7C01%7C%7C1f9b140e6bbf4da524c708d7cac0de99%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637200802027160487&sdata=EW1W6sxEg5ZkOxJ67KrQpBoI%2F7JYGTdTkrSZiboQbmA%3D&reserved=0
best,
Andre
On Tue, Mar 17, 2020 at 2:14 PM Alex <alexanderwien2k at gmail.com> wrote:
> Any comment, please?
>
> Thank you,
> Alex
>
> ---------- Forwarded message ---------
> From: Alex <alexanderwien2k at gmail.com>
> Date: Sun, Mar 15, 2020 at 8:16 PM
> Subject: Reproducibility of a PMF plot
> To: <gmx-users at gromacs.org>
>
>
> Dear all,
>
> Of course it is always good to prove that a MD simulation is reproducible
> by repeating several replicas of a simulation and then average over the
> quantity of interest, specially for a publishable result.
> I wonder if that also is necessary for a potential of mean force (PMF)
> calculation using umbrella sampling in which the bootstrap analysis is
> performed to calculate the standard deviation?
> Or for an alchemical free energy calculation where the e.g. the block
> averaging is used?
>
> Regards,
> Alex
> --
> Gromacs Users mailing list
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--
_____________
Prof. Dr. Andr? Farias de Moura
Department of Chemistry
Federal University of S?o Carlos
S?o Carlos - Brazil
phone: +55-16-3351-8090
------------------------------
Message: 5
Date: Tue, 17 Mar 2020 19:49:31 +0000
From: Poncho Arvayo Zatarain <poncho_8629 at hotmail.com>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] About membrane leaflets and msd
Message-ID:
<BN6PR08MB3618C7B7BA750901C7EB394580F60 at BN6PR08MB3618.namprd08.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Hello gromacs users: I want to obtain the lateral diffusion for a membrane with approximately 55 lipids+ions (NA+Cl) but i want to this for each leaflet of the membrane (outter and inner) and then obtain the average. I know that i can use gmx msd for lateral diffusion, but i don know how to know wich lipids are in each leaftlet. ?How can separate the leaflets to know wich lipid are in each one? After ?Can i make an index for each P molecule in each lipid for example and then use it in the gmx msd?
Thanks
------------------------------
Message: 6
Date: Tue, 17 Mar 2020 22:14:48 +0000
From: Poncho Arvayo Zatarain <poncho_8629 at hotmail.com>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] About gmx msd and membrane leaflets
Message-ID:
<BN6PR08MB3618A5591A3A882061AA3B7680F60 at BN6PR08MB3618.namprd08.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Hello gromacs users: I want to obtain the lateral diffusion for a membrane with approximately 55 lipids+ions (NA+Cl) but i want to this for each leaflet of the membrane (outter and inner) and then obtain the average. I know that i can use gmx msd for lateral diffusion, but i don know how to know wich lipids are in each leaftlet. ?How can separate the leaflets to know wich lipid are in each one? After ?Can i make an index for each P molecule in each lipid for example and then use it in the gmx msd?
Thanks
------------------------------
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